A comparative genomics multitool for scientific discovery and conservation

Diane P. Genereux; Aitor Serres; Joel Armstrong; Jeremy Johnson; Voichita D. Marinescu; Eva Murén; David Juan; Gill Bejerano; Nick Casewell; Leona G. Chemnick; Joana Damas; Federica Di Palma; Mark Diekhans; Ian T. Fiddes; Manuel Garber; Vadim N. Gladyshev; Linda Goodman; Wilfried Haerty; Marlys L. Houck; Robert Hubley; Teemu Kivioja; Klaus Peter Koepfli; Lukas F.K. Kuderna; Eric S. Lander; Jennifer R.S. Meadows; William J. Murphy; Will Nash; Hyun Ji Noh; Martin Nweeia; Andreas R. Pfenning; Katherine S. Pollard; David A. Ray; Beth Shapiro; Arian F.A. Smit; Mark S. Springer; Cynthia C. Steiner; Ross Swofford; Jussi Taipale; Emma C. Teeling; Jason Turner-Maier; Jessica Alfoldi; Bruce Birren; Oliver A. Ryder; Harris A. Lewin; Benedict Paten; Tomas Marques-Bonet; Kerstin Lindblad-Toh; Elinor K. Karlsson

doi:10.1038/s41586-020-2876-6

A comparative genomics multitool for scientific discovery and conservation

Diane P. Genereux, Aitor Serres, Joel Armstrong, Jeremy Johnson, Voichita D. Marinescu, Eva Murén, David Juan, Gill Bejerano, Nick Casewell, Leona G. Chemnick, Joana Damas, Federica Di Palma, Mark Diekhans, Ian T. Fiddes, Manuel Garber, Vadim N. Gladyshev, Linda Goodman, Wilfried Haerty, Marlys L. Houck, Robert HubleyTeemu Kivioja, Klaus Peter Koepfli, Lukas F.K. Kuderna, Eric S. Lander, Jennifer R.S. Meadows, William J. Murphy, Will Nash, Hyun Ji Noh, Martin Nweeia, Andreas R. Pfenning, Katherine S. Pollard, David A. Ray, Beth Shapiro, Arian F.A. Smit, Mark S. Springer, Cynthia C. Steiner, Ross Swofford, Jussi Taipale, Emma C. Teeling, Jason Turner-Maier, Jessica Alfoldi, Bruce Birren, Oliver A. Ryder, Harris A. Lewin, Benedict Paten, Tomas Marques-Bonet, Kerstin Lindblad-Toh, Elinor K. Karlsson

Tropical Disease Biology

Research output: Contribution to journal › Article › peer-review

227 Citations (Scopus)

Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

Original language	English
Pages (from-to)	240-245
Number of pages	6
Journal	Nature
Volume	587
Issue number	7833
DOIs	https://doi.org/10.1038/s41586-020-2876-6
Publication status	Published - 11 Nov 2020

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Genereux et al 2020 A comparative genomics Nature-Nov-20Final published version, 181 KBLicence: CC BY

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Genereux, D. P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V. D., Murén, E., Juan, D., Bejerano, G., Casewell, N., Chemnick, L. G., Damas, J., Di Palma, F., Diekhans, M., Fiddes, I. T., Garber, M., Gladyshev, V. N., Goodman, L., Haerty, W., Houck, M. L., ... Karlsson, E. K. (2020). A comparative genomics multitool for scientific discovery and conservation. Nature, 587(7833), 240-245. https://doi.org/10.1038/s41586-020-2876-6

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title = "A comparative genomics multitool for scientific discovery and conservation",

abstract = "The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80\% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.",

author = "Genereux, \{Diane P.\} and Aitor Serres and Joel Armstrong and Jeremy Johnson and Marinescu, \{Voichita D.\} and Eva Mur{\'e}n and David Juan and Gill Bejerano and Nick Casewell and Chemnick, \{Leona G.\} and Joana Damas and \{Di Palma\}, Federica and Mark Diekhans and Fiddes, \{Ian T.\} and Manuel Garber and Gladyshev, \{Vadim N.\} and Linda Goodman and Wilfried Haerty and Houck, \{Marlys L.\} and Robert Hubley and Teemu Kivioja and Koepfli, \{Klaus Peter\} and Kuderna, \{Lukas F.K.\} and Lander, \{Eric S.\} and Meadows, \{Jennifer R.S.\} and Murphy, \{William J.\} and Will Nash and Noh, \{Hyun Ji\} and Martin Nweeia and Pfenning, \{Andreas R.\} and Pollard, \{Katherine S.\} and Ray, \{David A.\} and Beth Shapiro and Smit, \{Arian F.A.\} and Springer, \{Mark S.\} and Steiner, \{Cynthia C.\} and Ross Swofford and Jussi Taipale and Teeling, \{Emma C.\} and Jason Turner-Maier and Jessica Alfoldi and Bruce Birren and Ryder, \{Oliver A.\} and Lewin, \{Harris A.\} and Benedict Paten and Tomas Marques-Bonet and Kerstin Lindblad-Toh and Karlsson, \{Elinor K.\}",

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doi = "10.1038/s41586-020-2876-6",

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Genereux, DP, Serres, A, Armstrong, J, Johnson, J, Marinescu, VD, Murén, E, Juan, D, Bejerano, G, Casewell, N, Chemnick, LG, Damas, J, Di Palma, F, Diekhans, M, Fiddes, IT, Garber, M, Gladyshev, VN, Goodman, L, Haerty, W, Houck, ML, Hubley, R, Kivioja, T, Koepfli, KP, Kuderna, LFK, Lander, ES, Meadows, JRS, Murphy, WJ, Nash, W, Noh, HJ, Nweeia, M, Pfenning, AR, Pollard, KS, Ray, DA, Shapiro, B, Smit, AFA, Springer, MS, Steiner, CC, Swofford, R, Taipale, J, Teeling, EC, Turner-Maier, J, Alfoldi, J, Birren, B, Ryder, OA, Lewin, HA, Paten, B, Marques-Bonet, T, Lindblad-Toh, K & Karlsson, EK 2020, 'A comparative genomics multitool for scientific discovery and conservation', Nature, vol. 587, no. 7833, pp. 240-245. https://doi.org/10.1038/s41586-020-2876-6

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AU - Genereux, Diane P.

AU - Serres, Aitor

AU - Armstrong, Joel

AU - Johnson, Jeremy

AU - Marinescu, Voichita D.

AU - Murén, Eva

AU - Juan, David

AU - Bejerano, Gill

AU - Casewell, Nick

AU - Chemnick, Leona G.

AU - Damas, Joana

AU - Di Palma, Federica

AU - Diekhans, Mark

AU - Fiddes, Ian T.

AU - Garber, Manuel

AU - Gladyshev, Vadim N.

AU - Goodman, Linda

AU - Haerty, Wilfried

AU - Houck, Marlys L.

AU - Hubley, Robert

AU - Kivioja, Teemu

AU - Koepfli, Klaus Peter

AU - Kuderna, Lukas F.K.

AU - Lander, Eric S.

AU - Meadows, Jennifer R.S.

AU - Murphy, William J.

AU - Nash, Will

AU - Noh, Hyun Ji

AU - Nweeia, Martin

AU - Pfenning, Andreas R.

AU - Pollard, Katherine S.

AU - Ray, David A.

AU - Shapiro, Beth

AU - Smit, Arian F.A.

AU - Springer, Mark S.

AU - Steiner, Cynthia C.

AU - Swofford, Ross

AU - Taipale, Jussi

AU - Teeling, Emma C.

AU - Turner-Maier, Jason

AU - Alfoldi, Jessica

AU - Birren, Bruce

AU - Ryder, Oliver A.

AU - Lewin, Harris A.

AU - Paten, Benedict

AU - Marques-Bonet, Tomas

AU - Lindblad-Toh, Kerstin

AU - Karlsson, Elinor K.

PY - 2020/11/11

Y1 - 2020/11/11

N2 - The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

AB - The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

U2 - 10.1038/s41586-020-2876-6

DO - 10.1038/s41586-020-2876-6

M3 - Article

SN - 0028-0836

VL - 587

SP - 240

EP - 245

JO - Nature

JF - Nature

IS - 7833

ER -

A comparative genomics multitool for scientific discovery and conservation

Abstract

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